I have a fancy for both the .338-06 and the .35 Whelen, but given that our choices are between the whelen and the 325WSM, I would vote for the Whelen. Remington now chambers the .35 Whelen in their CDL, and it looks really nice.
As far as factory ammo goes, God only knows what will happen to the .325WSM in 5 or 10 years. The whelen, on the other hand, while not popular by any strech of the imagination, still has a constant and predictable demand.
Zachary